.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M3562_626x4716_2007.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 3996 patterns found. (out of a total of 4716 sites) . 944 sites without polymorphism (20.02%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 1337Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 289 sec) [ -170160.0112] [GTR parameters ] . ( 307 sec) [ -168202.0618] [Alpha ][ 0.500960] . ( 310 sec) [ -168202.0618] [Topology ] . ( 488 sec) [ -161901.0040] [Topology ] . ( 670 sec) [ -159853.5244] [Topology ] . ( 856 sec) [ -158979.5463] [Topology ] . ( 1044 sec) [ -158559.4137] [Topology ] . ( 1233 sec) [ -158347.2387] [Topology ] . ( 1424 sec) [ -158207.3232] [Topology ] . ( 1616 sec) [ -158102.9965] [Topology ] . ( 1807 sec) [ -157917.5632] [Topology ] . ( 1998 sec) [ -157419.7976] [Topology ] . ( 2286 sec) [ -156559.7279] [GTR parameters ] . ( 2297 sec) [ -156543.4364] [Alpha ][ 0.461952] . ( 2300 sec) [ -156543.4364] [Topology ] . ( 2491 sec) [ -156184.0561] [Topology ] . ( 2682 sec) [ -156155.9813] [Topology ] . ( 2873 sec) [ -156145.9204] [Topology ] . ( 3063 sec) [ -156147.7791] [Topology ] . Moving backward . ( 3071 sec) [ -156132.0979] [Topology ] . ( 3261 sec) [ -156129.8023] [Topology ] . ( 3451 sec) [ -156129.1514] [Topology ] . ( 3641 sec) [ -156127.8614] [Topology ] . ( 3832 sec) [ -156126.0791] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4836 sec) [ -156123.2451] [Topology ] . ( 4917 sec) [ -156123.0219] [GTR parameters ] . ( 4926 sec) [ -156122.2019] [Alpha ][ 0.470633] . ( 4929 sec) [ -156122.2019] [Topology ] . ( 5120 sec) [ -156121.3493] [Topology ] . ( 5310 sec) [ -156120.8465] [Topology ] . ( 5501 sec) [ -156121.2415] [Topology ] . Moving backward . ( 5509 sec) [ -156118.8224] [Topology ] . ( 5700 sec) [ -156118.6457] [Topology ] . ( 5890 sec) [ -156118.5778] [Topology ] . ( 6081 sec) [ -156118.5480] [Topology ] . ( 6271 sec) [ -156118.5388] [Topology ] . Checking for NNIs, optimizing five branches... . ( 7083 sec) [ -156117.9455] [Topology ] . ( 7117 sec) [ -156117.9301] [GTR parameters ] . ( 7126 sec) [ -156117.9015] [Alpha ][ 0.472127] . ( 7130 sec) [ -156117.9015] [Topology ] . ( 7320 sec) [ -156117.4320] [Topology ] . ( 7511 sec) [ -156117.3957] [Topology ] . ( 7702 sec) [ -156117.4074] [Topology ] . Moving backward . ( 7710 sec) [ -156117.2778] [Topology ] . ( 7900 sec) [ -156117.2650] [Topology ] . ( 8091 sec) [ -156117.2575] [Topology ] . ( 8284 sec) [ -156117.2521] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9091 sec) [ -156116.7802] [Topology ] . ( 9113 sec) [ -156116.7774] [GTR parameters ] . ( 9121 sec) [ -156116.7774] [Alpha ][ 0.472127] . ( 9124 sec) [ -156116.7774] [Topology ] . ( 9315 sec) [ -156108.7079] [Topology ] . ( 9506 sec) [ -156107.0613] [Topology ] . ( 9696 sec) [ -156106.9071] [Topology ] . ( 9887 sec) [ -156106.8829] [Topology ] . (10078 sec) [ -156106.8785] [Topology ] . (10268 sec) [ -156106.8777] [Topology ] . Checking for NNIs, optimizing five branches... . (11074 sec) [ -156106.3044] [Topology ] . (11096 sec) [ -156106.3029] [GTR parameters ] . (11104 sec) [ -156106.3029] [Alpha ][ 0.472127] . (11107 sec) [ -156106.3029] [Topology ] . (11298 sec) [ -156103.9558] [Topology ] . (11488 sec) [ -156101.5759] [Topology ] . (11679 sec) [ -156101.2341] [Topology ] . (11869 sec) [ -156101.1309] [Topology ] . (12060 sec) [ -156101.0820] [Topology ] . (12250 sec) [ -156101.0576] [Topology ] . (12440 sec) [ -156101.0440] [Topology ] . Checking for NNIs, optimizing five branches... . (13246 sec) [ -156100.6867] [Topology ] . (13280 sec) [ -156100.6795] [GTR parameters ] . (13288 sec) [ -156100.6678] [Alpha ][ 0.471260] . (13291 sec) [ -156100.6678] [Topology ] . (13482 sec) [ -156100.6578] [Topology ] . (13672 sec) [ -156100.6600] [Topology ] . Moving backward . (13680 sec) [ -156100.6245] [Topology ] . (13870 sec) [ -156100.6207] [Topology ] . (14060 sec) [ -156100.6196] [Topology ] . (14251 sec) [ -156100.6193] [Topology ] . Checking for NNIs, optimizing five branches... . (15056 sec) [ -156100.2634] [Topology ] . (15079 sec) [ -156100.2633] [GTR parameters ] . (15086 sec) [ -156100.2624] [Alpha ][ 0.470788] . (15090 sec) [ -156100.2624] [Topology ] . (15280 sec) [ -156100.1401] [Topology ] . (15471 sec) [ -156100.1171] [Topology ] . (15661 sec) [ -156100.0795] [Topology ] . (15851 sec) [ -156099.0287] [Topology ] . (16042 sec) [ -156096.7327] [Topology ] . (16232 sec) [ -156094.3657] [Topology ] . (16422 sec) [ -156093.5079] [Topology ] . (16613 sec) [ -156093.3903] [Topology ] . (16803 sec) [ -156093.3670] [Topology ] . Checking for NNIs, optimizing five branches... . (17818 sec) [ -156093.1789] [Topology ] . (17840 sec) [ -156093.1776] [GTR parameters ] . (17848 sec) [ -156093.1773] [Alpha ][ 0.471322] . (17852 sec) [ -156093.1773] [Topology ] . (18043 sec) [ -156093.1367] [Topology ] . (18235 sec) [ -156093.1313] [Topology ] . (18429 sec) [ -156093.1312] [Topology ] . Checking for NNIs, optimizing five branches... . (19254 sec) [ -156092.5523] [Topology ] . (19276 sec) [ -156092.5518] [GTR parameters ] . (19284 sec) [ -156092.5518] [Alpha ][ 0.471322] . (19287 sec) [ -156092.5518] [Topology ] . (19479 sec) [ -156092.4250] [Topology ] . (19670 sec) [ -156092.1430] [Topology ] . (19861 sec) [ -156090.6252] [Topology ] . (20053 sec) [ -156086.0187] [Topology ] . (20249 sec) [ -156083.4673] [Topology ] . (20444 sec) [ -156082.9703] [Topology ] . (20641 sec) [ -156082.8729] [Topology ] . Checking for NNIs, optimizing five branches... . (21466 sec) [ -156082.6992] [Topology ] . (21488 sec) [ -156082.6986] [GTR parameters ] . (21496 sec) [ -156082.6986] [Alpha ][ 0.471322] . (21499 sec) [ -156082.6986] [Topology ] . (21693 sec) [ -156081.3705] [Topology ] . (21890 sec) [ -156081.1994] [Topology ] . (22086 sec) [ -156081.1782] [Topology ] . (22285 sec) [ -156081.1944] [Topology ] . Moving backward . (22293 sec) [ -156081.0955] [Topology ] . (22487 sec) [ -156081.0905] [Topology ] . (22679 sec) [ -156081.0894] [Topology ] . Checking for NNIs, optimizing five branches... . (23528 sec) [ -156081.0192] [Topology ] . (23551 sec) [ -156081.0189] [GTR parameters ] . (23559 sec) [ -156081.0189] [Alpha ][ 0.471322] . (23562 sec) [ -156081.0189] [Topology ] . (23763 sec) [ -156080.9726] [Topology ] . (23957 sec) [ -156080.9685] [Topology ] . (24153 sec) [ -156080.9683] [Topology ] . Checking for NNIs, optimizing five branches... . (24991 sec) [ -156080.9673] [Topology ] . (25014 sec) [ -156080.9672] [GTR parameters ] . (25021 sec) [ -156080.9672] [Alpha ][ 0.471322] . (25025 sec) [ -156080.9672] [Topology ] . (25219 sec) [ -156080.9615] [Topology ] . (25414 sec) [ -156080.9169] [Topology ] . (25609 sec) [ -156080.7600] [Topology ] . (25803 sec) [ -156080.6670] [Topology ] . (25998 sec) [ -156080.6167] [Topology ] . (26193 sec) [ -156080.5852] [Topology ] . Checking for NNIs, optimizing five branches... . (27014 sec) [ -156079.5284] [Topology ] . (27036 sec) [ -156079.5283] [GTR parameters ] . (27044 sec) [ -156079.5283] [Alpha ][ 0.471322] . (27047 sec) [ -156079.5283] [Topology ] . (27238 sec) [ -156079.3636] [Topology ] . (27428 sec) [ -156079.3462] [Topology ] . (27619 sec) [ -156079.3461] [Topology ] . Checking for NNIs, optimizing five branches... . (28445 sec) [ -156079.3461] [GTR parameters ] . (28453 sec) [ -156079.3461] [Alpha ][ 0.471322] . (28456 sec) [ -156079.3461] [Topology ] . (28646 sec) [ -156079.3500] [Topology ] . Moving backward . (28654 sec) [ -156079.3273] [Topology ] . (28845 sec) [ -156079.3266] [Topology ] . Checking for NNIs, optimizing five branches... . (29672 sec) [ -156079.3266] [GTR parameters ] . (29680 sec) [ -156079.3266] [Alpha ][ 0.471322] . (29683 sec) [ -156079.3266] [Topology ] . (29874 sec) [ -156079.3264] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -156079.326408. . Printing the most likely tree in file 'nucleic_M3562_626x4716_2007.phy_phyml_tree.txt'... . Time used 8h45m9s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 31584.75user 0.00system 8:47:30elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps